Evolution by means of natural selection

Main articles: Evolution and Darwinism

A prerequisite for natural selection to result in adaptive evolution, novel traits and
speciation, is the presence of heritable genetic variation that results in fitness differences.
Genetic variation is the result of mutations, recombinations and alterations in the
karyotype (the number, shape, size and internal arrangement of the chromosomes). Any
of these changes might have an effect that is highly advantageous or highly
disadvantageous, but large effects are very rare. In the past, most changes in the genetic
material were considered neutral or close to neutral because they occurred in noncoding
DNA or resulted in a synonymous substitution. However, recent research suggests that
many mutations in non-coding DNA do have slight deleterious effects.[16][17] Although
both mutation rates and average fitness effects of mutations are dependent on the
organism, estimates from data in humans have found that a majority of mutations are
slightly deleterious.[18]

The exuberant tail of the peacock is thought to be the result of sexual selection by
females. This peacock is an albino; selection against albinos in nature is intense because
they are easily spotted by predators or are unsuccessful in competition for mates.

By the definition of fitness, individuals with greater fitness are more likely to contribute
offspring to the next generation, while individuals with lesser fitness are more likely to
die early or fail to reproduce. As a result, alleles which on average result in greater fitness
become more abundant in the next generation, while alleles which generally reduce
fitness become rarer. If the selection forces remain the same for many generations,
beneficial alleles become more and more abundant, until they dominate the population,
while alleles with a lesser fitness disappear. In every generation, new mutations and re-
combinations arise spontaneously, producing a new spectrum of phenotypes. Therefore,
each new generation will be enriched by the increasing abundance of alleles that
contribute to those traits that were favored by selection, enhancing these traits over
successive generations.

Some mutations occur in so-called regulatory genes. Changes in these can have large
effects on the phenotype of the individual because they regulate the function of many
other genes. Most, but not all, mutations in regulatory genes result in non-viable zygotes.
Examples of nonlethal regulatory mutations occur in HOX genes in humans, which can
result in a cervical rib[19] or polydactyly, an increase in the number of fingers or toes.[20]
When such mutations result in a higher fitness, natural selection will favor these
phenotypes and the novel trait will spread in the population.

X-ray of the left hand of a ten year old boy with polydactyly.

Established traits are not immutable; traits that have high fitness in one environmental
context may be much less fit if environmental conditions change. In the absence of
natural selection to preserve such a trait, it will become more variable and deteriorate
over time, possibly resulting in a vestigial manifestation of the trait, also called
evolutionary baggage. In many circumstances, the apparently vestigial structure may
retain a limited functionality, or may be co-opted for other advantageous traits in a
phenomenon known as preadaptation. A famous example of a vestigial structure, the eye
of the blind mole rat, is believed to retain function in photoperiod perception.[21]

[edit] Speciation

Main article: Speciation

Speciation requires selective mating, which result in a reduced gene flow. Selective
mating can be the result of 1. Geographic isolation, 2. Behavioral isolation, or 3.
Temporal isolation. For example, a change in the physical environment (geographic
isolation by an extrinsic barrier) would follow number 1, a change in camouflage for
number 2 or a shift in mating times (i.e., one species of deer shifts location and therefore
changes its "rut") for number 3.[citation needed]

Over time, these subgroups might diverge radically to become different species, either
because of differences in selection pressures on the different subgroups, or because
different mutations arise spontaneously in the different populations, or because of
founder effects – some potentially beneficial alleles may, by chance, be present in only
one or other of two subgroups when they first become separated. A lesser-known
mechanism of speciation occurs via hybridization, well-documented in plants and
occasionally observed in species-rich groups of animals such as cichlid fishes.[22] Such
mechanisms of rapid speciation can reflect a mechanism of evolutionary change known
as punctuated equilibrium, which suggests that evolutionary change and particularly
speciation typically happens quickly after interrupting long periods of stasis.

Genetic changes within groups result in increasing incompatibility between the genomes
of the two subgroups, thus reducing gene flow between the groups. Gene flow will
effectively cease when the distinctive mutations characterizing each subgroup become
fixed. As few as two mutations can result in speciation: if each mutation has a neutral or
positive effect on fitness when they occur separately, but a negative effect when they
occur together, then fixation of these genes in the respective subgroups will lead to two
reproductively isolated populations. According to the biological species concept, these
will be two different species.